Generated summary
PXD057554 is a DDA label-free dataset (Mus musculus) with 8 runs, 8 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 69,522 PSMs, 5,699 peptidoforms and 720 protein groups, and the repository holds 2,646 PTM sites for it. 7 open warnings about it are recorded.
Written from catalog fields only (D17), with no model involved. It says nothing the tables below do not.
Written from catalog fields only (D17), with no model involved. It says nothing the tables below do not.
Open findings
Recorded against this dataset: 0 errors, 7 warnings and 1 for information
count_mismatch warning
The bundle holds 69522 where the producer reported 69523 (results.txt: All target PSMs with q-value <= 0.01 (pxreprise:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.
The bundle holds 69522 where the producer reported 69523 (results.txt: All target PSMs with q-value <= 0.01 (pxreprise:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.
high_contamination warning
5.08% of protein intensity in the worst file, 0.33% median across 8 files (DEF-QC-9 v3.5)
5.08% of protein intensity in the worst file, 0.33% median across 8 files (DEF-QC-9 v3.5)
low_core_use warning
8.23 avg cores of 32 allowed (S5)
8.23 avg cores of 32 allowed (S5)
low_id_rate warning
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 69523/529225 = 13.14% of MS2 identified (S3)
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 69523/529225 = 13.14% of MS2 identified (S3)
no_sdrf warning
No SDRF was found for this dataset, so each run was given a synthetic sample of its own. There is no sample metadata: treat every sample as unannotated.
No SDRF was found for this dataset, so each run was given a synthetic sample of its own. There is no sample metadata: treat every sample as unannotated.
occupancy_not_stored warning
Of 3006 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1029 site not in ptm_sites. 'site not in ptm_sites' means the entry's site has no ptm_sites row to key on; 'not determinable' means a cell's segments could not be assigned to its accessions from the sequences (QuantProject DEF-OCC-ACCESSION), which is never guessed. Absence of a row for these sites is therefore not NA. A 'duplicate' is a second entry for a (site, run) that already has a row: one with identical values loses nothing; one with DIFFERENT values means MetaMorpheus wrote two answers and the first in file order was stored (examples in bundle.json occupancy.differing_duplicates; which one should be stored is QuantProject's to define).
Of 3006 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1029 site not in ptm_sites. 'site not in ptm_sites' means the entry's site has no ptm_sites row to key on; 'not determinable' means a cell's segments could not be assigned to its accessions from the sequences (QuantProject DEF-OCC-ACCESSION), which is never guessed. Absence of a row for these sites is therefore not NA. A 'duplicate' is a second entry for a (site, run) that already has a row: one with identical values loses nothing; one with DIFFERENT values means MetaMorpheus wrote two answers and the first in file order was stored (examples in bundle.json occupancy.differing_duplicates; which one should be stored is QuantProject's to define).
unplaced_ptm_sites warning
Some modifications on peptides shared between proteins were not written to ptm_sites for one or more of those proteins, because the peptide could not be located in that protein's sequence and the producer's residue spans cannot be paired with its accessions. Of the (PSM, protein) pairs affected: 296 named a protein that does not contain the stored peptide -- typically a PSM ambiguous between peptide sequences (level 4 or 5), where this protein carries a different candidate than the first, which is the one stored. Sites on the other proteins of the same PSMs are written. Counts are in bundle.json under protein_databases.
Some modifications on peptides shared between proteins were not written to ptm_sites for one or more of those proteins, because the peptide could not be located in that protein's sequence and the producer's residue spans cannot be paired with its accessions. Of the (PSM, protein) pairs affected: 296 named a protein that does not contain the stored peptide -- typically a PSM ambiguous between peptide sequences (level 4 or 5), where this protein carries a different candidate than the first, which is the one stored. Sites on the other proteins of the same PSMs are written. Counts are in bundle.json under protein_databases.
occupancy_decoy_groups info
53 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
53 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
What was found
| PSMs at 1% FDR | 69,522 |
| Peptidoforms at 1% FDR | 5,699 |
| Protein groups at 1% FDR | 720 |
| PTM sites | 2,646 |
| Quantitative values | 57,565 |
| PSMs, all (including decoys and sub-threshold) | 842,057 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 13.1% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.5% |
How it was measured
- Organism searched
- Mus musculus (the protein database's organism, not a statement about the samples)
- Acquisition
- DDA
- Quantification
- label_free
- Labelling
- none
- Enrichment
- none
- Instrument vendor
- not recorded
- Runs / samples
- 8 / 8
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 6ea39b9e1b3a
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 1,608 |
| Oxidation on M | UNIMOD:35 | 510 |
| Hydroxylation on P | UNIMOD:35 | 91 |
| Phosphoserine on S | UNIMOD:21 | 61 |
| N-acetylalanine on A | UNIMOD:1 | 57 |
| 4-hydroxyproline on P | UNIMOD:35 | 46 |
| Acetylation on X | UNIMOD:1 | 34 |
| N-acetylmethionine on M | UNIMOD:1 | 26 |
| Hydroxylation on K | UNIMOD:35 | 21 |
| N-acetylserine on S | UNIMOD:1 | 21 |
| N6-acetyllysine on K | UNIMOD:1 | 14 |
| Phosphorylation on S | UNIMOD:21 | 11 |
| Acetylation on K | UNIMOD:1 | 10 |
| HexNAc on S | UNIMOD:43 | 9 |
| Deamidated asparagine on N | UNIMOD:7 | 7 |
| Methylation on K | UNIMOD:34 | 7 |
| N6-methyllysine on K | UNIMOD:34 | 7 |
| HexNAc on T | UNIMOD:43 | 6 |
| N-acetylthreonine on T | UNIMOD:1 | 6 |
| Phosphorylation on T | UNIMOD:21 | 6 |
| Phosphothreonine on T | UNIMOD:21 | 6 |
| N-myristoyl glycine on G | UNIMOD:45 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| 3-hydroxyproline on P | UNIMOD:35 | 3 |
| Dimethylation on R | UNIMOD:36 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| Omega-N-methylarginine on R | UNIMOD:34 | 3 |
| Pros-methylhistidine on H | UNIMOD:34 | 3 |
| Trimethylation on K | UNIMOD:37 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| Allysine on K | UNIMOD:352 | 2 |
| Dimethylation on K | UNIMOD:36 | 2 |
| Glutarylation on K | UNIMOD:1848 | 2 |
| N-acetylvaline on V | UNIMOD:1 | 2 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 2 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 2 |
| N6-succinyllysine on K | — | 2 |
| Phosphotyrosine on Y | UNIMOD:21 | 2 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 1 |
| Butyrylation on K | UNIMOD:1289 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Dimethylated arginine on R | UNIMOD:36 | 1 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 1 |
| Hydroxybutyrylation on K | — | 1 |
| Methylation on R | UNIMOD:34 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylglycine on G | UNIMOD:1 | 1 |
| Phosphorylation on Y | UNIMOD:21 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| S-geranylgeranyl cysteine on C | UNIMOD:48 | 1 |
| Succinylation on K | UNIMOD:64 | 1 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 1 |
Every modification with a site on a target protein, most frequent first. A dash in the UNIMOD
column means the modification has no UNIMOD term in the registry that searched it, not that it is
unknown. One chemistry can appear under two names (UniProt's and MetaMorpheus's); the catalog's
ptm_sites_by_chemistry view merges them.
Data
The Parquet files for this dataset are not published yet.
- Bundle
67b01d35db14198e, written 2026-10-29T12:29:19+00:00 by ingester 1.4.0- Reconciliation
- failed: psms_target_1pct (the bundle disagrees with the producer's own count here)
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group